hi @KarelOtruba
You seem to have a decent grasp on what you want. Theres no right or wrong ways. Its all down to your requirements.
But as you asked this is my take on inventory:
inventory is basically storage, an array. So while it might be advantagous to have some interactivity like potion use, or item equip from inside the inventory. I would keep it simple as possible.
As far as auto using items, i would have equipment slots like most games do.
so say you have 2 weapon slots, if one is empty when picking up a weapon, put it in the slot, otherwise the inventory. Same with potions. This helps keep things easier to manage and not over complicate. Then you can assign keys or action to those slots as you wish that then access the items inner workings.
So you want someway of identifying what an item is and does and a way of communicating its actions without having to spawn the item. OR spawn the item in your hand and let the actor object handle its workings. which might be easier as the first option is kinda duplicating work.
As far as the node, you could have a spawner that spawns the node after x time after its destroyed (if its renewable of not then just place them).
Inside the actual crystalnode actor handle dropping of crystals depeding on an event or interaction with the player. Once the node is empty then destroy the actor and no more crystals can be gotten as it was the crystalnode actor handling the drops.